™

Mass Spec Results Analysis Tool—MSRAT bioinformatics software

™M RATbioinformatic oftware

Introducing■ INSTANT DISCOVERYFind biomarkers hidden in your data at the click of the mouse

■ INSTANT ANALYSISPowerful comparative analysis with virtual 3D and differential heat maps

■ INSTANT CONFIDENCEData fi lters, replicate analysis and peptide coverage maps insures robust, reliable conclusions

The Power of Proteomics Unleashed

Import Search Results File Discover Biomarkers

M RAT Workflow

Protein Viewer

MW

M RAT Bioinformatics oftware

The full biological impact of Mass Spec based proteomics is often obscured in the very large data sets that are generated. This means that the full meaning of a given experiment cannot be appreciated without significant bioinformatics and statistical processing effecting both the quality and pace of discovery. MSRAT™ bioinformatics software empowers the proteomics researcher by eliminating these barriers:

■ Highlight data trends instantly with visualization tools ■ Enhance discovery power with real-time interactive data query ■ Enable easy, label-free comparisons of quantitative differences

between samples■ Facilitate deeper analysis to find post-translational

modifications, when pI data from the digital ProteomeChip™ is used.

■ Find biomarkers like a pro with interactive graphing, heat maps and Venn diagrams

■ Combine replicates to improve the quality of your biomarker calls

www.proteinforest.com

Instant Analysis, Discovery and Confidence

Discover what you have been missing…

MSRAT™ bioinformatics software enables

the proteomic researcher to focus on

the biological significance of their data

immediately. Simply load your search

data (~3 – 4 minutes), assign experimental

information and explore the biological

results.

The advanced visualization, sorting, filtering

and analysis provide incredible discovery

power! It is now possible to interactively

query your data in real-time at the click of

the mouse. This not only gets the most out

of your current data but speeds you towards

your next discovery.

Additional power for discovery is achieved

when isoelectric point (pI) data, highlighting

post-translational modifications, is added

from proteins or peptides that have been

separated using the digital ProteomeChip™

platform.

The MSRAT software and digital Proteome-

Chip system will allow you to ‘see important

results that you were missing before’.

Download a free demo today and see for yourself!

Discover Biomarkers Report Findings

3D Differential Map

pI

Getting to your results requires considerable effort and bioinformatics expertise before even knowing that your experiment worked, not to mention finding important information buried in the data. Further experiments can be delayed by weeks and months while the data is being analyzed. MSRAT™ bioinformatics software will get you from ‘click to conclusion’ using your mouse. With one mouse click you can:

■ Exclude protein ID’s made with fewer than 2, 3 or 4 unique peptides

■ Exclude redundant proteins■ Exclude Keratin■ Export data to MS Excel or XML ■ Calculate differential scores■ Determine peptide coverage■ Sort any column of data ■ Process replicates

You will instantly find potential biomarkers between samples using the 3D differential map tool. This tool uses protein ID, MW and pI data to generate a map that instantly reveals the most differential proteins. The size of the circle is proportional to the magnitude of the differential score. The color of the circle, red or blue, indicates the up or down expression of a protein. Simply click on a circle to reveal detailed protein information.

experience MSrAT™ for yourSelf wiTh A free deMo AT

www.proTeinforeST.coM

617.926.4778www.proteinforest.com

Your Next Discovery is a Mouse-Click Away

Finding Biomarkers in Your Data has Never Been This Easy

Discover what you have been missing…

Discover biomarkers in your data with the 3D Differential Map

Underexpressed

Overexpressed

MW

pI

Protein Forest, Inc.Ledgemont Center

128 Spring St.Lexington, MA 02421

617.926.4778

www.proteinforest.com

MSRAT™ Software: requirementsProcessor Dual Core 2.6 GHzRAM 1GB (for Windows) 2GB (for Vista) 2GB or higher recommendedMonitor Resolution 1024 x 768 or higherOperating System Windows XP (Service Pack 2) Windows VistaInstallation CD-ROM / Internet downloadMicrosoft Office™ Excel XP or newerInternet Browser Internet Explorer 6 or newerInternet Connection RequiredHard disk Space Required 250 Mb Free spaceInput File Type Excel or XML files from Sequest, MASCOT, Scaffold or Custom

© 2008 Protein Forest Inc. All rights reserved. These products are supplied for research, laboratory or manufacturing applications only. Visit our website for up to date prices. digital ProteomeChip™ technology is covered by U.S. Patent 7,166,202, foreign equivalents and other patent applications pending. All trademarks are property of Protein Forest Inc.

Visual Tools Protein Viewer Peptide Viewer Protein Database Viewer Differential Heat map 3D Differential Map Venn Diagram Interactive Charting ■ Bar ■ Line ■ PieFiltering Tools Exclude ■ Keratin ■ Redundant proteins ■ Protein ID’s made with fewer than 2, 3 or 4 unique peptides

Data Analysis Tools Process replicates Consolidate peptides Calculate differential scores Sort any column of data Export data to MS Excel or XML Determine peptide coverage

MSRAT™ Software: major features